FME installs its own Python interpreter, which is used by any scripts that run Python in FME. If you want FME to use your own custom Python interpreter, run the following commands from a command prompt:
<FMEServerDir>Server/fme/fme.exe APPLY_SETTINGS SYSTEM "Python/Use Custom Python" true
<FMEServerDir>Server/fme/fme.exe APPLY_SETTINGS SYSTEM "Python/Python Interpreter" c:/<path_to_dll>/python27.dll